rs7117074

Variant names:

• chr11-30964540-A-C
• rs7117074
• NM_001387274.1:c.2592-11972T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387274.1(DCDC1):​c.2592-11972T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,916 control chromosomes in the GnomAD database, including 18,873 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (18873 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 2 publications found

Genes affected

DCDC1 (HGNC:20625): (doublecortin domain containing 1) This gene encodes a member of the doublecortin family. The protein encoded by this gene is a hydrophilic, intracellular protein. It contains a single doublecortin domain and is unable to bind microtubules and to regulate microtubule polymerization. This gene is mainly expressed in adult testis. It does not have a mouse homolog. [provided by RefSeq, Sep 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.2592-11972T>G		intron_variant	Intron 20 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.2592-11972T>G		intron_variant	Intron 20 of 38		NM_001387274.1	ENSP00000507427.1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72731 AN: 151798 Hom.: 18866 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.508

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.479 AC: 72760 AN: 151916 Hom.: 18873 Cov.: 32 AF XY: 0.474 AC XY: 35169 AN XY: 74226

African (AFR) AF: 0.293 AC: 12140 AN: 41472

American (AMR) AF: 0.466 AC: 7097 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2202 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1512 AN: 5146

South Asian (SAS) AF: 0.512 AC: 2462 AN: 4812

European-Finnish (FIN) AF: 0.495 AC: 5222 AN: 10550

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40305 AN: 67932

Other (OTH) AF: 0.513 AC: 1079 AN: 2104

Alfa AF: 0.534 Hom.: 8386

Bravo AF: 0.467

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.75
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7117074; hg19: chr11-30986087;